Omics approaches employed to study biological molecules have revolutionized environmental microbiology and elevated our understanding of ecological processes in the biosphere. However, conventional omics applications often lead to the loss of information about macromolecular organization of the molecules within the cellular context. This can be a significant disadvantage since many proteins are functional only as macromolecular complexes in particular structural forms. A great example is bacterial contractile injection system (CIS), a syringe-like protein complex whose function is the translocation of molecules into a target cell to affect its state, often inducing lysis. Since the function of CIS is tightly linked to its intracellular localization, proteomics cannot confidently predict the function of novel uncharacterized CISs in natura. To overcome this challenge, we have developed a cryo-electron tomography workflow as a technique complementing metagenomics and proteomics. Additionally, we developed an immuno-electron microscopy protocol to identify and quantify CIS particles in environmental samples. Using this approach, we discovered a novel bacterial CIS in thermophilic multicellular Chloroflexota bacteria populating hot spring mats worldwide. We found that this system is similar phylogenetically and structurally to a recently described cytoplasmic CIS, which was found in multicellular Streptomyces and has been shown to be involved in cell cycle regulation. Interestingly, using our approaches, we have discovered that Chloroflexota cells produce different numbers of CIS particles depending on the mat micro-niches they occupy. In agreement with this, we observed that CIS was also non-constitutively expressed under laboratory conditions. Motivated by this discovery, we searched and analyzed similar CIS in extremophilic bacteria from other lineages. Overall, we have gained an understanding that bacterial cytoplasmic CIS is an overlooked cellular feature of the extremophilic bacteria, which is potentially involved in the cell fate control or intraspecies interaction within microbial community.

Brucellosis is an infectious disease spread around the world. It is a zoonosis transmitted to humans by animals they are working with closely, such as cattle, sheep and even dogs.
Brucella bacteria are host specific, but they can end up in humans as incidental hosts through the digestive or respiratory tract. Once in the host, Brucella are internalised into the Brucella containing vacuole (BCV). BCVs initially follow the canonical endocytic trafficking, fusing first with early, then late endosomes, followed by limited fusion with lysosomes. During this last step transient acidification triggers the T4SS leading to effector translocation and trafficking into the ER. Upon reaching the ER the BCV converts from its non-replicative state to the replicative state. During the endocytic path, Brucella escape host recognition and interact with the immune system of the host. Furthermore, they seem to be resistant to the complement system.
The major part of Brucella-host interaction is believed to be via proteins secreted into the host cells, so called effectors. Effectors known interact with parts of immune recognition. Due to several challenges with Brucella, not many effectors are known yet. Up until now, only biased approaches were used for the identification.
Bio-orthogonal non-canonical amino acid tagging (BONCAT) can be used as an unbiased approach to identify the secretome of Brucella using mass spectrometry. It allows identification of effectors of Brucella at different times during the infection process.
Due to the high genetic similarity of the Brucella species, BSL2+ classified species B. microti can be used as a surrogate to the BSL3 classified species B. abortus.

The Gram-negative, facultative intracellular zoonotic pathogen Brucella spp. cause the debilitating disease Brucellosis. Brucella, as an intracellular pathogen, encounters various stressful environments while being trafficked towards the replicative niche inside the host cell, which it either has to withstand or counteract. We aimed at understanding the contribution of the putative Type 4 secretion system effector BspD to intracellular survival and replication. To this end we used in silico analyses, classical growth curves and axenic stress assays, as well as host cell infection. We show that BspD is a conserved protein of the Rhizobiales, which does not show signs of co-evolution with the presence of a T4SS or a certain lifestyle. Further, using in vitro assays we show that BspD is critical for Brucella abortus envelope integrity in the stationary phase and in the presence of EDTA, a compound known to destabilize the outer membrane. Deletion of bspD resulted in abnormal bacterial morphologies, indicating its involvement in maintaining envelope integrity. In infection the absence of BspD led to the formation of fewer and smaller intracellular microcolonies in a macrophage infection model. From our observations, we propose that BspD of B. abortus is critical for preserving the integrity of the bacterial envelope, particularly under stressful conditions, which may enhance Brucella’s ability to survive within host cells independently of its putative status as a Type 4 secretion system effector.

Understanding the interactions between bacterial plant pathogens and their natural antagonists is essential for establishing sustainable agricultural practices. This study expands our knowledge about the mechanisms behind the antagonistic interaction between Erwinia tasmaniensis, a non-pathogenic member of the flower microbiome, and Erwinia amylovora, the causative agent of fire blight in rosaceous hosts (e.g apple, pear, quince). E. tasmaniensis is believed to interfere with the pathogen proliferation in the flower and thus with infection, so we characterized novel strains isolated from a fire blight-free orchard where it was previously shown to dominate (Gschwend 2021).

Comparative genomic analysis including our isolates and publicly available E. tasmaniensis and E. amylovora genomes, revealed a high degree of interspecies (83%) and intraspecies similarity (>99%), including a conserved core carbon metabolism. Notably, variable gene content was associated with functions like plasmid transfer, bacterial competition (T6SS, R-M systems, and toxin-antitoxin systems), and peripheral carbon utilization. To further explore these differences, a phenotypic microarray analysis using 191 metabolites was employed to characterize the carbon source utilization profiles of nine E. tasmaniensis strains and a representative E. amylovora strain (LMG1893). This analysis identified significant disparities in carbon source utilization and metabolic pathways between the two bacterial species, with substantial phenotypic variation observed within E. tasmaniensis itself.

Based on our integrated findings, we conclude that E. amylovora and E. tasmaniensis compete for nutrients present in flower stigma exudates, including simple sugars (glucose, fructose, sucrose) and complex carbohydrates (pectin, hemicellulose, arabinogalactan). The observed greater metabolic versatility of E. tasmaniensis in utilizing these floral metabolites may provide a competitive advantage over E. amylovora during flower colonization. This phenomenon holds promise for the development of novel biocontrol strategies to combat fire blight.

While the majority of people exposed to Salmonella will likely develop gastroenteritis, a small proportion of the population (< 1%) will become asymptomatically colonised. We are interested in characterising the composition of the gut microbiota profile of asymptomatic Salmonella carriers as compared to symptomatic Salmonella patients and healthy controls, to understand the mechanisms which protect against a symptomatic infection.
The faecal samples from 9 non-typhoidal infected Salmonella patients, 23 asymptomatic Salmonella carriers, and 11 healthy individuals were collected. Their profiles were characterised by evaluating the 16S rRNA amplicon sequences, genomic variation, and functions predicted using 16S rRNA data.
The most common strain identified was serovar Typhimurium. Statistically, no significant difference in the presence of antimicrobial resistance genes, virulence genes, and plasmid replicons between the symptomatic and asymptomatic groups were observed. Both groups displayed similar levels of alpha diversity, which was statistically lower to healthy individuals. A significant PERMANOVA indicated that all profiles were statistically distinct from one another. Healthy and asymptomatic individuals possessed higher prevalence of bacteria belonging to the Lachnospiraceae, Ruminococcaeae, and Christensenellaceae family. Five species were identified as being differentially enriched in the asymptomatic group compared to the symptomatic group, of which four species belong to the Lachnospiraceae and Ruminococcaeae family. Compared to the symptomatic profile, the asymptomatic profile saw an increase in predicted functions associated with degradation and biosynthesis. Community profiling identified three clusters within our samples, where profiles resembled a eubiotic, dysbiotic, and intermediate profile. The eubiotic community saw an enrichment in functions associated with biosynthesis compared to the dysbiotic community.
The lack of significant differences among the virulence of the strains suggests that virulence may not play a role in influencing a symptomatic profile. Differential abundance analysis and bacterial prevalence imply symptomatic patients lack bacteria from the the Lachnospiraceae and Ruminococcaeae family, bacteria which have been reported to be positively associated with gut health. Future studies will focus on identifying a bacterial consortium and challenging Salmonella in mice to evaluate their protective potential.

Agrochemicals are key stressors affecting the health of bees and other pollinators. While incidences of bee mortality linked to acute pesticide exposure are well studied, sub-lethal pesticide exposure has now been shown to depress immunocompetence, pathogen resistance, and foraging behavior. These same traits are modulated by the specialized microbial communities in the gut of social bees. Therefore, investigating the mechanistic interplay between agrochemicals, bees and their microbiota is crucial to understand the full impact of chronic, sub-lethal exposure that is now common across diverse ecosystems. Limited findings already indicate that the honeybee gut microbiota is both perturbed by certain pesticides, while also biochemically altering others. Whether these microbial biotransformation’s are beneficial or harmful to their bee host remains unknown. Unfortunately, the vast array of agrochemicals makes comprehensive experiments documenting interactions with microbes in the bee gut nearly impossible.

We propose high-throughput, in vitro screens as tools to identify agrochemicals that are either highly toxic to the gut microbiota, or that are biotransformed by the microbiota. The resulting positive hits can then be further validated using laboratory or field trials of managed and wild bees. As a first step in this effort, we report the toxicity of 1054 pesticides, antibiotics, and other agrochemicals towards 20 bacterial strains grown in isolation and in synthetic communities. These strains encapsulate the species level diversity within the gut of the western honeybee (Apis mellifera). We identified 126 compounds (12% of the panel) that were toxic to one or more strains at environmentally relevant concentrations (≤ 20 μM). Amongst the largest chemical classes in our screen, fungicides were substantially more likely to be toxic to the microbiota (6% of interactions) than herbicides or fungicides (1% of interactions). We further exposed the microbiota to a subset (656 agrochemicals) of the original panel and measured their degradation using high resolution LC-MS. Here we identified 55 chemicals (8% of the panel) that were significantly degraded by at least one strain.

Our results demonstrate the feasibility and utility of high-throughput screens to rapidly identify microbial interactions with agrochemicals, and they pave the way for further targeted experiments with high likelihood of finding microbiome mediated effects on the honeybee host.

Service-learning is a teaching and learning method that combines community service and education. It allows students to actively apply the knowledge acquired during their curriculum to address real-world societal issues. In the “Microbes go to school” program proposed by UniNE, students from bachelor and doctoral school programs visit classes to explain topics related to microbiology to children aged 6-12. The goal is to use alternative didactic approaches to teach a topic that is not covered in school. During the 2024 spring semester, a service-learning activity was implemented to explain the problems posed by the excessive development of toxigenic cyanobacteria in water bodies. This is linked to a real-world issue that has affected the Canton of Neuchâtel and other Cantons in recent years. Since 2020, in the region near the Areuse river, several dogs died after the ingestion of microbial mats composed mainly of benthic cyanobacteria. These events have created apprehension in residents about their security near recreational places along the river and shores of Lake Neuchâtel. As a result, misinformation about cyanobacteria emerged. It appeared therefore crucial to inform people about the real associated risks. For this, we created an activity to explain and present cyanobacteria to children of 4th grade (7-8 years old). The activity spreads over 4 days (2 hour/days) and was presented as a game in which children acted as detectives to discover the microorganism who had killed the dogs. At the beginning of the activity, four different suspects were presented to children (a virus, cyanobacteria, green algae, and bacteria). The activity included theory, a field excursion, and a visit of the University laboratory. During these sessions, the children had to collect clues to identify the microorganism responsible for the dogs' death. Some of the clues were given during theoretical lessons, while others were deduced from their observations in the field or during the laboratory session. With this activity, children acquired knowledge in microbiology including aspects of the ecology of the suspected microorganisms. To verify the knowledge acquired, a poster summarizing the activity was created by children. In addition to the impact on the public, the activity allowed the University students who set it up to gain knowledge about scientific communication and to develop effective communication tools to explain a societal issue in a pragmatic and entertaining manner.

Aims The inappropriate use of antibiotics in human medicine has exacerbated the threat of antimicrobial resistance (AMR). Urgent action is required to raise awareness among prescribers about the significance of judicious antibiotic use. Innovative educational tools tailored to accommodate their limited time availability for training could prove more effective in improving antibiotic prescribing practices.
Methods To mark the World Antibiotic Awareness Week 2023, the Infection Prevention and Control units (IPC) of the Canton of Vaud and CHUV developed a virtual game titled "Mission Antibiotix." This game was made freely accessible online and specifically aimed at hospital physicians. The educational materials were crafted by physicians from the two IPC units, with support from the AMR taskforce of CHUV. Game development was undertaken by the Continuing Education Center of the CHUV and a communication specialist from the cantonal IPC unit. Players were invited to immerse in a set of realistic clinical scenarios. They were tasked with making appropriate prescribing decisions by searching for clues in virtual patient rooms, all within a time limit of 20 minutes. Immediate feedback was provided following each decision-making moment. At the CHUV, the game was organized as interdepartmental championships in auditoriums or incorporated into internal postgraduate trainings. Meanwhile, the individual mode was used in other hospitals across Vaud. An evaluation form was accessible on the game's website for feedback.
Results Since its launch, the website has garnered over 850 visits. During the CHUV championship, 30 teams comprising over 135 players from 15 different wards participated over four days, engaging in four very lively meetings held either in auditoriums or during ward meetings. Feedback from the 82 championship participants was extremely positive, with many emphasizing the interactivity and realism of the chosen cases. 73% of players believed they have acquired knowledge useful to their practice.
Conclusion This serious game encouraged physicians' involvement, thanks to its playful approach and accurate representation of clinical reality. Its easy integration into their work schedule, along with its short duration, contributed to increased engagement. Additionally, playing as a team in a collaborative environment facilitated message anchoring. Finally, the platform's flexibility allows for future updates in content and target audience.

Background: VIRTUE, a virtual reality hand hygiene trainer, offers users the option of visualizing pathogen transfers during virtual patient care either in ‘real-time’ or at the end of a run as a ‘summary’ visualization. In this study, we aimed to evaluate the effect of different timings of pathogen visualisation (‘real-time’ vs. ‘summary’) on in-trainer performance and user’s immersion.
Methods: The study included first-year medical students undergoing hand hygiene training with VIRTUE, randomized to one of three visualization set-ups: set-up 1 (“on-off-off”, with ‘real-time’ visualisation at the first level only, and ‘summary’ visualization at level 2 and 3), set-up 2 (“off-on-off”), and set-up 3 (“off-off-off”). In-trainer performance was defined by number of pathogen transmission events (=contaminations) in level 3. The virtual experience of user’s (among others: immersion) was assessed with a questionnaire.
Results: 173 medical students participated in the study, with 58, 54, and 61 assigned to set-up 1, set-up 2, and set-up 3, respectively. Users assigned to set-up 3 with ‘summary’ visualization at all levels, performed best with 1.02 (SD +/- 1.86) contaminations, compared to 2.34 (SD +/- 3.09) and 2.07 (SD +/- 2.52) contaminations of users assigned to the other set-ups. ‘Summary’ visualization at all levels also resulted in higher immersion of users.
Conclusions: ‘Real-time’ visualization of pathogen transmission during virtual reality hand hygiene training with VIRTUE can affect in-trainer performance and user immersion. This emphasizes the importance of pilot testing the effect of VR-based trainings in order to understand the impact of the virtual reality on users.

Aims
Isolation precautions and their implementation are crucial aspects of an infection prevention team's daily responsibilities. This task is often repetitive and time-consuming, as the necessary information is scattered across various documents. We aim to develop a chatbot powered by generative AI that can efficiently answer standard questions about isolation precautions.

Methods
The core information source is derived from the comprehensive documents prepared by the infection prevention team. These documents encompass a detailed list of indications for isolation precautions and exhaustive guidance on how to implement various types of isolation measures effectively.
Using this information, a generative AI model is trained to address queries related to known pathogens only. In instances where a scenario is not covered in the existing documentation, the AI is designed to refer back to the infection prevention team for expert advice.
The model's responses are supported by direct links to the pertinent documents, ensuring accuracy and relevance.

Outcomes
We are evaluating the feasibility of deploying a chatbot tailored to provide guidance on isolation precautions. Our primary goal is to create a model that consistently offers precise and reproducible responses, each traceable back to its original document. The model is designed to eliminate any inaccuracies and halluzinations and will refer to human experts in infection prevention for queries concerning unknown pathogens. This project is a proof of concept; thus, results will be limited to those obtained from a controlled testing environment, as real-world data will not be available at the time of this abstract's presentation. Additionally, we explore the time required for development, necessary technical expertise, and associated costs.

Conclusions
We believe that generative AI holds immense potential in everyday clinical medicine. Most hospitals have internal guidelines on a variety of topics, and infection prevention measures, being highly standardized and consistent, are ideal for testing the capabilities of such artificial support systems. If the proof-of-concept proves successful, there is potential for expansion into numerous other areas.

Background: Diagnostic stewardship (DS) in diagnostic microbiology (DM) aims at optimizing the ordering process for microbiological analyses. We present the first evaluation of DS rule algorithm incorporation in the digital order entry process (DOEP) for DM at our tertiary care hospital.

Methods: DS rule algorithms (RA), based on in-house guideline for DM, focus on frequent analyses with low pre-test probability or unnecessary repetitiveness. During a pilot phase of nine months (June 2023 to February 2024), we addressed 1.) blood cultures (BC), 2.) serostatus with prior positive finding and 3.) PCR for viruses in blood without prior positive serostatus.
Rule algorithms are based upon 1.) the priorly published Shapiro-Procalcitonin algorithm (SPA) for BC, and 2./3.) queries of prior positive serological findings. Background algorithms of the DOEP integrate clinical and laboratory findings within predefined time frames. The ordering person is guided through the algorithm during ordering process resulting in a recommendation for (positive) or against the test (negative). This recommendation can be overruled.
Rates of followed recommendations (positive or negative) and overruling are monitored according to professional state of the ordering person (physician vs. non-physician).

Results: 22'057 activated algorithms consisted of 19'289 (87.4%) followed positive, 1'109 (5.0%) followed negative and 1'659 (7.6%) overruled recommendations. For 2'541 BC algorithms, rates for negative recommendations and overruling were 25.8% and 24.8% respectively, for 18'170 serostatus 1.3% and 3.4% respectively and for 1'346 PCRs 16.7% and 30.2% respectively. Considering negative recommendations as prevented unnecessary analyses, 229 serologies, 225 PCRs and 655 BC could be saved.
Of all orders, 79.9% were done by physicians and 20.1% by non-physicians. For non-physicians, the odds ratios (OR) for both generating negative and overruled recommendations were increased (2.9-6.5). Especially Hepatitis B- and Hepatitis C-PCR RA showed high rates of overrulement by non- physicians belonging to distinctive departments and wards (53.0% and 53.4% of all overruled specific RA, respectively).

Conclusions: RA for DOEP can support and monitor evidence based ordering behaviour for microbiological analyses, reduce unnecessary analyses, identify critcal organisation units causing excessive redudancy and hence, potentially save resources and costs.

Für die Desinfektion der Haut vor der Einlage eines peripheren Venenverweilkatheters (PVK)können verschiedene Substanzen verwendet werden. In kontrollierten StudienA konnte gezeigt werden, dass die Hautdesinfektion mit 2% Chlorhexidine Gluconate - Alkohol 2% (CHG) gegenüber Isopropylalkohol 70% (IPA) hinsichtlich infektiösen Komplikationen von Vorteil ist. Wir wollten wissen, ob die Umstellung der routinemässigen Desinfektion der Einstichstellen vor der Einlage eines PVK) von IPA auf CHG mit einer Reduktion der lokalen Komplikationen assoziiert ist und damit die bisher gezeigten Vorteile aus Studien im klinischen Alltag eines Spitals reproduziert werden können.
Ziel: Der Vergleich der lokalen Komplikationsrate der PVK- Insertionsstellen vor und nach der Umstellung der Desinfektion von IPA auf CHG.
Methode: Eine Single-Center-Qualitätssicherungsstudie. Intervention war die Einführung von CHG auf allen Abteilungen. Outcome war das Auftreten einer lokalen Komplikation (eiternd, gerötet, Verhärtung der Vene) der Einstichstellen nach Einlage eines PVK. Sämtliche Patienten mit PVK wurden während der Beobachtungszeit nach internem Standard regelmässig monitorisiert, allfällige lokalen Komplikationen wurden systematisch dokumentiert. Ein Poisson Regressionsmodell wurde angewendet um das monatliche Inzidenzratenverhältnis vor und nach der Intervention zu vergleichen.
Ergebnisse: Wir haben total 35’681‬ Patienten nach Einlage eines PVKs überprüft. 24`369 in der IPA-Gruppe (Jan 2021 – Jan 2023), 11`312 in der CHG-Gruppe (Feb 2023 - Jan 2024). Frauen waren in der IPA Gruppe mit 53.8% vertreten, in der CHG-Gruppe mit 54.6%. Das mediane Alter betrug 67 (52-77, IPA) resp. 66 Jahre (52-77, CHG). Die Beobachtungsdauer betrug in beiden Gruppen im Median 2 Tage. Die Rate an beobachteten, kumulativen Veränderungen betrug 322 (1.3%) in der IPA Gruppe resp. 119 (1.1%) in der CHG Gruppe (p = 0.036). Die Verteilung der einzelnen Befunde in der IPA respektive CHG Gruppe war wie folgt: Eiternd: 4 (0.0%) versus 0 (0.0%) (p = 0.409), gerötet: 238 (1.0%) versus 95 (0.8%) (p = 0.233), verhärtet: 103 (0.4%) versus 29 (0,3%) (p = 0.021). Das Inzidenzratenverhältnis für alle Komplikationen nach der Einführung betrug 0.79 (95% CI, 0.64 - 0.97; p = 0.03).
Konklusion: Die Umstellung von IPA auf CHG als Desinfektionsmittel zur Vorbeugung von unerwünschten Ereignissen durch das Einsetzen von PVC war mit einer signifikanten Reduktion der auffälligen Katheter Einstichstellen assoziiert. Die a

BACKGROUND AND AIM: Valais ranks second highest canton in antibiotic prescriptions for outpatient care in Switzerland (Swiss Health Observatory data). To tackle this public health concern, a cantonal plan aligning with the National Antibiotic Resistance Strategy (StAR) is underway. An evaluation phase is currently ongoing to tailor the plan to local needs.
METHODS: A 35-questions survey administered via RedCap® was emailed to all physicians practicing in Valais (~1300). Survey was available online from 22 November 2023 to 15 February 2024, with data collection conducted anonymously. Statistical analysis was performed in Stata. Ambulatory and in-hospital physicians answers were compared using Chi2 tests and Student-t tests.
RESULTS: 305 surveys were completed (response rate~23%), 53.1% (n=162) by women and 45.2% (n=138) by men. Participants working in outpatient settings (n=163) were significantly older than those working in hospitals (n=172) (49.3 vs 41.7 years on average, p < 0.001). Main reasons to prescribe antibiotics were. were urinary tract (reported by 70.9% of the physicians) and lower respiratory tract infections (63.7%). Major barriers to responsible antibiotic prescribing include patient pressure (47.5%), diagnostic difficulty (36.6%), and lack of continuing education (17.3%). Outpatient physicians reported more patient pressure (62.4% vs 31.0%), p < 0.001), while in-hospital physicians identified lack of ongoing education more frequently as a barrier to responsible antibiotic prescription (24.5% vs 11.5%, p = 0.003). In-hospital physicians consulted specialists more (48.1% vs 22.9%, p < 0.001), while outpatient practitioners relied on experience (54.2% vs 27.5%, p < 0.001). In-hospital physicians showed more interest in a smartphone application (49.7% vs 27.3%, p < 0.001). About half of the respondents (n=153) indicated missing resources to inform their patients about antibiotics. The majority of the respondents, 75.4% (n=230), felt that a public campaign would be relevant to increase population awareness and knowledge. Physicians highlighted the importance of utilizing social media (70.5%) and involving schools (45.5%).
CONCLUSION: Awareness of StAR resources for patient education seems limited. Tailoring interventions to meet the diverse needs of physician groups, addressing resource constraints and knowledge gaps, is crucial for effective implementation. A population survey is ongoing in Valais and both will guide implementation strategies

Gene Transfer Agents (GTAs) are mobile genetic elements mediating horizontal gene transfer in bacteria and archaea. GTAs originate from bacteriophages that over time got “domesticated” by the cells and at present transfer random parts of the bacterial genome and are unable to self-propagate.
An interesting example is BaGTA (Bartonella GTA) present in bacteria Bartonella. BaGTA is highly conserved and emerged from two sequential domestications of phages which resulted in acquisition of the GTA locus forming the capsid and run-off replication (ROR) amplifying DNA prior to the packaging.
Both GTA and ROR are functionally linked and contribute to the gene transfer. However, little is known how both clusters cross-regulate. To address this, we assess how genes in the ROR (brrA, brrG, brrB) and orphan genes (bgtS, bgtTUV) are regulated and how they impact the GTA cluster transcription. For that, we harness methods of mass-spectrometry, flow cytometry and sequencing to investigate protein-protein interactions and unveil gene regulation.
GTAs are widespread in bacteria and archaea we believe it could be a fourth major mechanism of horizontal gene transfer that might drive evolution of their hosts.

Bacteriophages, the viruses infecting bacteria, represent the most abundant biological entities on Earth and hold great promise as alternative therapeutics for multidrug-resistant bacterial infections. Despite their potential, our understanding of the molecular mechanisms underlying phage-host interactions has been primarily confined to a few classical phage models. This not only restricts the immediate application of findings in phage therapy but also indicates that a vast reservoir of potent molecular biology within the natural diversity of bacteriophages remains untapped.
To address this gap, we have composed the BASEL (Bacteriophage Selection for your Laboratory) collection, a reference set of 105 newly isolated Escherichia coli phages extensively characterized through genomic and phenotypic analyses. Importantly, our upcoming expansion pack highlights previously overlooked phage groups, notably those that depend on LPS O-antigen glycans as host receptors absent in laboratory E. coli strains. Additionally, we isolated phages from rare groups susceptible to the resident bacterial immunity of E. coli K-12. Our findings demonstrate how the assorted diversity of phages can be leveraged to systematically uncover the molecular mechanisms underlying host recognition and resistance to bacterial immunity systems. These insights are directly informative for the selection of phages for clinical or biotechnological applications.
The BASEL collection has already been shared with multiple laboratories worldwide, serving as a valuable tool in exploring different aspects of phage-host interactions. Taken together, this work bridges the gap between model phages and the incredible diversity of phages in nature, offering crucial insights for both clinical applications and fundamental phage biology.

Aims: Bacteriophages, or viruses that infect bacteria, are teeming with genes of unknown function. These accessory genes are often thought to code for diverse products, including toxins and virulence factors. These could pose problems when applying phages in a therapeutic setting. Therefore, we need a rapid and efficient method to delete these problematic phage accessory genes.

Methods: We focus on a modified Type I-C CRISPR-Cas3 system, also known as haCas3, to make small deletions in Pseudomonas aeruginosa phages. Together with a series of crRNAs, we can use the haCas3 system together with its wild-type counterpart to rapidly establish the essentiality of every hypothetical protein-coding gene in a phage genome, and isolate mutants lacking these genes.

Results: We were able to isolate mutants for the temperate virus JBD68 and therapeutic candidate Pb1. The haCas3 system produces random deletions within the range of around 10-3,000 bp without the need for a repair template. With this system we were able to map the essentiality of all the hypothetical protein coding genes in JBD68, and produce a minimal genome JBD68 by deleting more than 3,000 bp from its genome.

Conclusion: We demonstrated the efficacy of the wild-type Cas3 system at targeting and degrading diverse phages, as well as the ability of the haCas3 system in producing deletions in genes of interest that allow the phages to escape wild-type Cas3 selection. We also generated a genome-minimised phage based on JBD68. With its reduced genome, payloads such as bacteriocins can be easily introduced that would enhance its therapeutic potential without worrying about the effect on genomic space. Overall, we provide a new tool that can be used for the study of phage accessory genes and for easy and efficacious phage genetic engineering.

Context and Aim:
The global rapid spread of antimicrobial resistance calls for urgent action. Phage therapy is seen as a promising alternative to the antibiotic use. Until now, phage therapy has relied on the use of cocktails of natural lytic bacteriophages against susceptible bacteria. However, this approach requires extensive screenings of phage collections and might also trigger phage resistance in target bacteria. Most lysogenic phages or prophages, integrated in the genomes of most multi-drug resistant (MDR) bacteria, already possess all the genetic elements required to infect and lyse their bacterial hosts. However, they cannot be used as effective therapeutics due to their non-lytic profiles and to the presence of undesirable cargo on some of their genomes (i.e. antimicrobial resistance or toxin-encoding genes). To solve these problems, we aim to develop a synthetic genomics pipeline employing the yeast Saccharomyces cerevisiae as an engineering platform to turn prophages into tailor-made lytic phages to be used for the treatment of infections caused by MDR bacteria, focusing on Klebsiella pneumoniae.
Methods:
We first performed whole genome sequencing of a subset of clinical Klebsiella pneumoniae strains and explored the diversity of their prophage content in silico. Then, we induced functional prophages using Mitomycin C and determined phage host-range against clinical strains. We used the yeast genetic platform and TAR cloning to modify phage genomes by removing genetic elements necessary for establishment of lysogeny.
Results:
We successfully induced and characterized prophage Φ3_19KM57, which showed lytic activity against a clinical MDR strain K. pneumoniae 06KM907. Thus, Φ3_19KM57 was selected for phage engineering. We were able to modify the genome of this phage by removing the integrase (int) and major lysogeny regulator (C2) genes, which are essential for viral genome integration and establishment of lysogeny, respectively. The newly engineered phage versions showed enhanced virulence towards susceptible K. pneumoniae strain 06KM907 and increased lytic activity.
Conclusion:
We believe that other prophages like Φ3_19KM57 could be similarly modified and used safely as alternative therapies to antibiotics to treat bacterial infections. Moreover, the same pipeline could be used to enhance phage virulence towards other MDR bacteria.

The globally endemic low pathogenic human coronavirus (HCoV) 229E has been circulating in the human population for a long time with little sequence alterations. HCoV-229E-like viruses have been found in bat species (BatCoVs) as well as dromedary camels (DcCoVs) exemplary DcCoV-ACN4. For HCoV-229E and 229E-like DcCoVs no recent zoonotic spillovers are documented. Genome analysis propose that HCoV-229E evolved from bats via dromedary camels. This evolutionary scenario shows strong parallels to the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV). MERS-CoV is a highly pathogenic zoonotic virus that sporadically spills over from the dromedary camel reservoir to humans with a 36% fatality rate. Like HCoV-229E, the origins of MERS-CoV have been linked to ancestral BatCoVs. Consequently HCoV-229E and DcCoV-ACN4 can provide important insight into how emerging CoVs like MERS-CoV cross the species barrier and adapt to the human species.
To analyze potential species barriers, we first investigated the spike-receptor interaction of HCoV-229E and DcCoV-ACN4. We used vesicular stomatitis virus (VSV) CoV-S pseudotyped viral particles on HEK cells overexpressing the human or dromedary camel aminopeptidase N; receptor for HCoV-229E. Then we assessed permissiveness by performing replication kinetics on species-specific cell lines. To mimic in vivo conditions, we further performed the replication kinetics on human (h) and camelid (c) primary airway epithelial cell (AEC) cultures. Proceeding Immunofluorescence staining imply adverse cell tropism for HCoV-229E in hAEC, DcCoV-ACN4 in cAEC and MERS-CoV in hAEC and cAEC.
We show an entry-independent species-restricted replication of HCoV-229E and DcCoV-ACN4 in AEC culture that was not observed for MERS-CoV. Our findings indicate that the observed species barriers of HCoV-229E and DcCoV-ACN4 lie beyond the spike-receptor interaction and open the search for the viral and host factors influencing the different host specificities of HCoV-229E, DcCoV-ACN4 and MERS-CoV.

Aims. Developing an in vivo model of intestinal colonization with multidrug-resistant E. coli (MDR-Ec). Moreover, testing bacteriophages as a possible decolonization strategy.

Methods. Zophobas morio larvae were colonized by implementing two different approaches. First, through contaminated food administration from T0 (day 0) to T7 with three MDR-Ec producing ESBLs and/or carbapenemases: Ec-4901.28 (ST131, CTX-M-15), Ec-042 (ST410, OXA-181) and Ec-050 (ST167, NDM-5). After T7, larvae received non-contaminated food until T28. In the second approach, force-feeding was performed to refine the model and expedite the experimental process using a single 5 µL 4901.28 at 108 CFU/mL per os injection on T0.
To detect MDR-Ec strains, larvae were homogenized at different time-points. Samples were plated on selective ChromID ESBL plates followed by 24 h incubation and colony count (CFU/mL). Decolonization using the INTESTI bacteriophage cocktail was performed by injecting 2 doses of 10 µL. Dynamic changes of Z. morio intestinal microbiota and resistome of challenged larvae were also investigated. Microbiota characterization was achieved through 16S rRNA amplicon sequencing and further diversity analyses were performed.
Results. With the first approach, contaminated food administration with the MDR-Ec strains induced rapid colonization with high bacterial load of ∼106-7 CFU/mL at T7. Larvae remained colonized with Ec-4901.28 and Ec-042 until T28 (103-4 CFU/mL). Larvae receiving a force-feeding treatment with bacteriophages were decolonized by Ec-4901.28 (INTESTI-susceptible); however, Ec-042 and Ec-050 (INTESTI-resistant) did not. Natural microbiota of Z. morio larvae was very rich of bacterial genera (i.e., Lactococcus, Enterococcus, Spiroplasma, Latilactobacillus). Moreover, Escherichia-Shigella genera appeared in larvae only at T7-T10. Notably, even for the second approach, force-feeding resulted in a colonization effect with 105 CFU/mL at T14.

Conclusion. Larvae possess a rich microbiota and can be easily colonized with global clones of MDR-Ec. Moreover, with the second approach we optimized the time required to induce intestinal colonization and retain a high bacterial load. Therefore, the Z. morio model presents a high-throughput compromise to study novel gut decolonization strategies reducing the number of subsequent mammalian experiments in line with the 3Rs strategy.

The Chlamydiales order contains obligate intracellular bacteria (such as Waddlia chondrophila and Chlamydia trachomatis) sharing a common biphasic developmental cycle characterized by infectious, non-replicative elementary bodies and non-infectious, replicative reticulate bodies. When exposed to stress stimuli, reticulate bodies enter a persistence state called aberrant bodies (ABs). ABs are believed to play a role in chronicity and recurrence of chlamydial infections.


RNA-sequencing performed on Waddlia aberrant bodies allowed us to identify ispA (iron starvation protein A), an upregulated gene in the Chlamydiae phylum, and exclusively present in that phylum. W. chondrophila and C. trachomatis ABs were then obtained with other types of stresses to assess the behavior of this gene. Bioinformatic and wet-lab analysis were also performed to characterize the protein.


We confirmed that while ispA is upregulated upon iron-starvation in W. chondrophila, it wasn’t the case for C. trachomatis. In fact, of all the stresses applied, heat-shock is the only tested condition where the upregulation was observed in both species. The secretion of IspA by the T3SS predicted bioinformatically was confirmed using Yersinia enterocolitica as heterologous system, but its localization within the host cell observed by immunofluorescence is unclear. Interestingly, IspA has a conserved C-terminal domain resembling that of a cystine-knot. Cystine-knots are described as a domain of protein interaction but was only described in eukaryotes. Regulation-wise, a conserved CIRCE sequence which allows repression by HrcA, a stress regulator, was identified upstream ispA.


Our preliminary results reveal IspA, a highly conserved, Chlamydiae-specific T3SS effector, with a conserved cystine-knot-like domain, and a conserved CIRCE regulatory sequence. Despite these conservations, ispA answers differently to various stresses across the phylum, but similarly to heat-shock for C. trachomatis and W. chondrophila. Further studies should aim at identifying IspA targets and other regulatory pathways to explain these discrepancies.

Intracellular bacteria manipulate and subvert cellular processes in their eukaryotic hosts in a sophisticated manner. The facultative intracellular pathogen Legionella pneumophila naturally replicates in free-living amoeba. Inhalation of this pathogen can lead to a severe pneumonia, due to its ability to replicate within alveolar macrophages. To this end, L. pneumophila secretes over 300 “effector proteins” into host cells, which subvert phagosome maturation and other cellular processes, eventually leading to the formation of a specific Legionella-containing vacuole (LCV). While LCV formation represents an essential step for the intracellular survival and replication of L. pneumophila, virtually all host cell processes are targeted and subverted during infection.
Mitochondrial function and dynamics are essential for basically all cellular processes. Previous studies have shown that L. pneumophila specifically targets and modulates mitochondrial components and their function. Using bioinformatic tools and experimental approaches, we identified and characterized in this project novel L. pneumophila effectors localizing to and targeting the mitochondrial network. Deletion mutants lacking single effector proteins showed an intracellular replication defect, indicating that the mitochondria-targeting effectors have important functions during infection. Some of these effectors were found to affect host cell respiration. Current studies aim at identifying the eukaryotic targets of these effectors and elucidating their mode of action.

Aims
Staphylococcus aureus has been causing invasive, difficult-to-manage conditions such as endocarditis and osteomyelitis. Certain strains have developed resistance to antibiotics thus making them more difficult to treat. Current strategies to detect Staphylococcus aureus infections and their antibiotic susceptibility require a culturing step prior to diagnosis and characterization. We aim to eliminate the need for bacterial culturing and hence, reduce the time to diagnosis to a few hours. We present a single-domain-antibody-based strategy to capture S. aureus from solution. We aim to capture S. aureus from the site of infection, thus enriching the bacteria over the patient material, and hence, facilitating diagnosis.

Methods
We screened our synthetic library for single-domain antibodies that specifically bind to surface proteins of S. aureus. We chose Staphylococcal surface protein A as a target due to its high abundance and sequence conservation across species. After screening the library for single-domain antibodies we then coupled selected antibodies to a commercially available maleimide-PEG11-biotin linker construct via cysteine-maleimide coupling chemistry. This capture molecule would be able to bind to the surface protein on S. aureus, and further, streptavidin-magnetic beads could be used to fish out the bacterial cells via biotin-streptavidin chemistry.

Results
Using our strategy, we were able to demonstrate successful capture of S. aureus from buffer solutions and growth medium within an hour of incubation with the capture molecules. We have observed a capture efficiency of approximately 60-80% for various lab strains and clinical isolates. Our capture strategy can specifically enrich S. aureus even when the bacterial count is as low as 500-1000 CFUs, mimicking an early stage of infection.

Conclusion
The presented method reduces the detection time from a full day to a few hours. Importantly, the isolated bacterial cells are preserved in their most natural state facilitating characterization of the infection and antibiotic susceptibility testing. With some optimization, our capture strategy may be able to significantly enrich S. aureus over human material from patient samples, ensuring ease of diagnosis. The presented strategy is a proof of concept and should passage the advent of rapid and reliable diagnosis of S. aureus infections.

Aims
The combination of IVD-R compliant 16S eubacterial PCR followed by Sanger sequencing enables a rapid, and cultivation-free identification of bacterial pathogens in clinical samples. With low biomass samples, Sanger sequencing is typically used given the expected lower diversity, lower cost, faster turnaround time, as well as simplified analysis, which usually outweigh the benefits of next-generation sequencing methods. Yet, Sanger sequencing often fails to resolve even low diversity microbial samples, spurring the need for cheap and more fine-grained technologies. Here, we present a novel approach coupling 16S eubacterial PCR with third-generation Oxford Nanopore Technologies (ONT) sequencing for clinical diagnostic applications.

Methods
To validate the specificity and sensitivity of our approach, we conducted comparative sequencing of 16S eubacterial PCR amplicons on both ONT and Illumina MiSeq platforms. Sequencing was performed on routine samples normally processed in our diagnostic department for eubacterial species presence. Reads obtained by both ONT and Illumina technologies underwent processing via the ONT-tailored LORCAN bioinformatic pipeline (1). To mitigate potential biases introduced by analyzing Illumina data with the LORCAN pipeline, Illumina read analysis was also validated with dada2 (2), a tool optimized for short-reads. Sensitivity was additionally assessed using dilution series of two bacterial species to confirm diagnostic performance.

Results
First results with a small sample set (about 40 samples) underscore the robustness and accuracy of ONT sequencing in capturing the diversity of clinical eubacterial samples. ONT sequencing followed by streamlined data analyses accelerates turnaround time to below one working day from samples to bioinformatic analyses, while maintaining cost efficiency, crucial for diagnostic applications. The higher resolution offered by ONT over Sanger sequencing provides a clear advantage for pathogen detection in complex or lowly concentrated microbial samples, as well as resolving bacterial background contamination.

Conclusion
The combination of 16S eubacterial PCR with ONT sequencing represents an important improvement in terms of sensitivity and specificity to Sanger sequencing, and leads to improved cost-effectiveness and turnaround time in clinical microbial diagnostics.

Background/Aims
Strongyloides stercoralis affects >100 million individuals worldwide, especially immunocompromised patients are at increased risk for severe infection. Therefore, all solid transplant (SOT) candidates are screened for S.stercoralis infection before transplantation and prophylactic treatment is administered if ELISA test results are positive. ELISAs for S.stercoralis tend to cross-react if subjects are infected with other (non-strongyloides) helminths and central/northern Europe is a low-endemic area for S.stercoralis Therefore, a relevant proportion of pre-transplant S.stercoralis ELISA results may reflect false positive results and patients will receive unnecessary treatment. We evaluated a two-step testing approach using an ELISA for screening and a Westernblot (WB) for confirmation of S.stercoralis infection.
Methods
We recently developed and validated a WB for detection of anti-S.stercoralis specific antibodies using well-defined reference patient sera. Subsequently, we performed a pilot study for the technical validation of the WB. For this, we used frozen serum samples of SOT candidates who previously underwent S.stercoralis testing (ELISA) as part of their pre-transplant workup between 2018 and 2022.
Results
The novel WB specifically detects human IgG antibodies (two immunodominant antigenic compounds of 12 and 17kDa) against S.stercoralis with a diagnostic sensitivity of 91% and a diagnostic specificity of 100%.
We tested 310 serum samples of which 8.7% (27/310) showed positive (>10AE/mL)- and 6.5% (20/310) revealed borderline (1-9AE/mL) S.stercoralis ELISA results. Analysis of the 47 ELISA positive/borderline samples with the WB revealed that 87.2% (41/47) of these tests were false-positive. Half (3/6) of WB positive samples showed borderline results in the ELISA screening.
Conclusion
The novel WB specifically detects S.stercoralis antibodies in serum of SOT candidates. Our results indicate that also borderline ELISA test results may represent true-positive findings. Therefore, the level (AE/mL) of S.stercoralis antibodies measured by ELISA should not be used as a proxy for differentiation of false-positive from true-positive tests. As present guidelines recommend to screen for S.stercoralis infection in SOT candidates using serologic assays only, no stool samples are available for these patients. A future clinical study will assess the sensitivity and specificity of a two-step approach for serologic S.stercoralis testing.

Background
Molecular methods have significantly improved tuberculosis (TB) diagnosis. However, to enhance the detection rate, current diagnostic process involves multi-test strategy often utilizing microscopy, PCR, and culture in successive clinical specimens especially in patients with paucibacillary disease. While, evaluating the performance of individual test is manageable, assessing the overall performance, including sensitivity and specificity, of a multi-test strategy is complex and prone to over or undertesting. In this study we aimed to develop and validate a model specifically designed to assess the performance of multi-test strategies for TB diagnosis.
Methods
Using a database encompassing 34’429 specimens and 14’358 patients from our tertiary care teaching hospital (2008-2018), we first determined the diagnostic performance of individual microbiological TB tests using multiple variables including type of test, type of clinical specimen, patient age and gender. Subsequently, we applied a Hidden Markov Models (HMM) to derive a score indicating a patient's TB likelihood based on sequential molecular test results (1, 2, 3 or more). Finally, we determined the performance of the prediction model against the historical database.
Results
We calculated TB prevalence and individual tests sensitivity and specificity across diverse categories, including gender (male/female), age (categorized into five groups), four distinct types of microbiological tests (microscopy, Xpert MTB/RIF or in-house real-time PCR, and culture), and four clinical specimen types (sputum, induced sputum, bronchoalveolar lavage and bronchial aspirate). Utilizing the overall sequence of PCR tests for each patient in our cohort, this information was employed in a Hidden Markov Model (HMM) to generate a probability score (ranging from 0 to 1) indicating the likelihood of having TB. Using a gold standard based on culture and clinical data, we established an optimal score of 0.995 at which, the sensitivity and specificity for predicting TB of the HMM was 95,7% and 97,9% respectively.
Conclusions
In this study, we developed and validated a model that calculate the performance of TB multiple test strategies that integrates the comprehensive history of molecular test results alongside patient-specific factors. This model could further enhance diagnostic algorithms, offering valuable support for clinical decision-making across different stages of multiple test strategies.

Introduction: Infective endocarditis (IE) is a rare disease with significant morbidity and mortality, experiencing shifts in epidemiology due to an aging population and an increasing use of endovascular devices. This study evaluates changes in microbiological trends and outcomes in patients with IE over a decade in Switzerland.
Methods: In this nationwide cohort study, we analyzed in-hospital claims data from patients hospitalized with IE in Switzerland between January 2012 and December 2021. We assessed the monthly case numbers and incidence rates per 100,000 hospitalizations, categorizing them by common pathogens (Staphylococcus aureus, other Staphylococcus species (spp.), Enterococcus spp., Streptococcus spp., gram-negative bacilli, HACEK [Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, and Kingella], pathogens of culture-negative IE, unknown pathogens, and other pathogens). Odds ratios (OR) or log-transformed gamma regression coefficients with corresponding confidence intervals (CI) were calculated to estimate the association between pathogens and outcomes. Main outcomes included all-cause in-hospital mortality, all-cause 6-month mortality, intensive care unit (ICU) admissions and length of hospital stay (LOS).
Results: Among 15,255 hospitalizations with IE, the annual number of cases increased from 1,361 in 2012 to 1,636 in 2021. Predominantly diagnosed pathogens were S. aureus (increasing from 19.8% in 2012 to 30% in 2021, p for trend < 0.01) and Streptococcus spp. (from 17.6% to 24.4%, p for trend < 0.01). IE caused by S. aureus was associated with the highest in-hospital (19.9%) and 6-month (30.3%) mortality rates and showed no significant trend over the decade. When compared to S. aureus, IE caused by HACEK (OR 0.23, 95% CI 0.11 to 0.48) or unknown pathogens (OR 0.21, 95% CI 0.18 to 0.24) had the lowest in-hospital mortality rates. Patients suffering from IE caused by an unknown pathogen were less likely being admitted to an ICU. The longest LOS was observed in IE hospitalizations with S. aureus (mean 23.79 days) and the shortest LOS in IE with unknown pathogens (-31.19%, p < 0.01).
Conclusion: This nationwide cohort study showed an increase in IE hospitalizations from 2012 to 2021, mainly caused by S. aureus and streptococci, particularly noting that S. aureus was associated with adverse outcomes, which remained unchanged over time, when compared to other or undiagnosed pathogens.

Aims
Since June 2022, an increase in Corynebacterium diphtheriae cases, mainly associated with migrant- related facilities, has been reported by the European Centre for Disease Prevention and Control. We present a cluster of genetically related strains of toxigenic C. diphtheriae causing infections in patients previously considered as being at low risk.
Methods
In October 2023, toxigenic C. diphtheriae was recovered from samples collected due to suspected infection from two patients hospitalized at two tertiary care centers within the city of Basel, Switzerland. Routinely performed whole genome sequencing revealed close genetic relatedness of the recovered strains, triggering a joint outbreak investigation involving the public health authorities.
Results
Patient A, a 78-year-old female was admitted due to acute respiratory failure related to suspected pneumonia. She died shortly after admission despite intensive care treatment. Toxigenic C. diphtheriae was cultured from the bronchial aspirate collected at admission. Her vaccination status remains unknown. Patient B, an 88-year-old male was admitted after biopsy of a chronic sacral wound showed growth of toxigenic C. diphtheriae. The patient improved after systemic antibiotic and local wound treatment and was discharged to a geriatric rehabilitation facility. He reportedly had not received any diphtheria vaccine since 1969 and the diphtheria antitoxin IgG level was < 0.1 IU/ml.
The two clinical isolates of C. diphtheriae were identified as ST574 and were genetically identical (zero allelic differences). Both isolates were closely related (one to five allelic differences) to a cluster of strains derived from five patients, all asylum seekers (AS) accommodated in a federal asylum center in Basel, from 2022.
The two current patients had no known interaction or epidemiologic link to each other or to the previously diagnosed cases and reported no travel history.
Conclusions
Toxigenic C. diphtheriae has emerged in Europe among populations typically not considered at risk – possibly facilitated by re-introduction of strains by migration and decreasing immunity due to lacking catch- up vaccination. This report calls for raised clinical and laboratory awareness for toxigenic C. diphtheriae infections and supports the promotion of respective vaccination regimens.

Aim. Trained immunity reflects the capacity of the innate immune system to adapt to an initial challenge and mount an improved response to a secondary challenge. The induction of trained immunity is associated with metabolic, epigenetic and functional reprogramming of stem cells, stromal cells and myeloid cells. We demonstrated that training protects mice from a wide range of bacterial infection (Ciarlo E. et al. J. Infect. Dis. 2020:222:1869). Surprisingly, while neutrophils play a key role in host defences, their role during training is poorly understood. We aimed to determine whether neutrophils are reprogrammed during training and to assess their role during streptococcal pneumoniae.

Methods. Mice were challenged with PBS (control) or β-glucan (training) given intraperitoneally. After one week, mice were sacrificed to collect organs and cells, or were challenged intranasally with Streptococcus pneumoniae with or without control or trained neutrophils. Samples were analysed by flow cytometry, scRNAseq and multiplex bead assay. Mouse morbidity and mortality were registered daily.

Results. Training increased bone marrow myeloid stem and progenitor cells, and immature and mature neutrophils in bone marrow, blood, spleen and lungs (P < 0.001). RNAseq demonstrated that the transcriptome of trained neutrophils was altered with gene pathways related to effector functions significantly enriched. In agreement, trained neutrophils showed increased chemotaxis, phagocytosis and S. pneumoniae-induced IL-1β, IL-6 and G-CSF production (P < 0.05). Training protected mice from lethal pneumococcal pneumonia. The protection was lost upon neutrophil depletion (0.0% versus 87.5% survival in neutrophil-depleted versus neutrophil-non-depleted trained mice, P < 0.001). The adoptive transfer of trained neutrophils to naive mice increased their resistance to S. pneumoniae infection.

Conclusions. Training triggered central and extramedullary hematopoiesis and elicited a marked rewiring of the neutrophil compartment. Neutrophils are altered upon training and play a key role in the protection against pneumococcal pneumonia. The molecular mechanisms underlying neutrophil reprogramming are under investigation.

Aim
Sepsis remains a critical global health challenge. Digital advancements offer new opportunities to improve patient’s management and outcome through enhanced data utilization and workflow automation. We thus aimed to deploy a digital pipeline to support and critically appraise a sepsis quality-of-care program.
Methods
We deployed in a tertiary care center (1500 beds) a fully automated pipeline extracting patient data from electronic health records as of November 2021. This digital pipeline feeds a dedicated registry for continuous monitoring of a sepsis care pathway (SCP). A Python-based pipeline extracts patient data from electronic health records within SCP-equipped units. Data goes through several processing scripts to compute clinical scores which are then stored in a dedicated registry within a data warehouse. The automatic generation of dynamically updated sepsis-specific indicators from the registry onto dashboards (e.g. time to antibiotics, in-hospital mortality) enables a continual assessment of the program’s performance over tunable periods with resolution to hospital units.
Results
We monitored from January 2022 to December 2023 through our pipeline 26,000 stays and documented and analyzed 252 sepsis cases. Of these, 139 were treated within the pathway (SCP) and 113 without the pathway (SCWP). Patients’ characteristics from SCP and SCWP groups were similar in age (median 67.545 vs. 66.547 p = 0.79), sex (74.8% vs. 65.5% males; p = 0.139). SCP had more chronic comorbidities than SCWP (median (IC 5 – 95%), Charlson comorbidity index 4.0 (0 – 12) vs. 2.0 (0 – 10), respectively p = 0.039). The fraction of sepsis patients receiving antibiotics within the recommended time frames according to the Surviving Sepsis Campaign was higher for SCPs than SCWP (antibiotics in < 1h, 23.4% vs. 11.6%, in 1 - 3h, 21.8% vs. 17.5%, and in > 3h 54.8% vs. 70.9% (p = 0.0281) for SCP vs. SCWP, respectively). Other indicators such as ICU transfers at 72 hours (36.7% vs. 45.1% for SCP vs. SCWP, respectively; p = 0.853) and in-hospital mortality (10.7% vs 16.8%) for SCP vs. SCWP, respectively; p = 0.228) trended lower in SCPs compared with SCWPs though not reaching statistical significance.
Conclusion
We have deployed a highly agile digital pipeline supporting the implementation and enabling the critical appraisal of a sepsis care pathway. Such an approach has the potential to be implemented – with suitable adaptations – to other institutions and/or acute pathologies.

Aims
Coinfections of Mycobacterium tuberculosis (MTB) and human immunodeficiency virus (HIV) impose a substantial global health burden. Patients with MTB infection face a heightened risk of progression to active TB, which preventive therapy can mitigate. Current testing methods often fail to identify individuals who subsequently develop active TB, particularly among people with HIV (PWH), necessitating a new testing approach.

Methods
We developed artificial intelligence (AI) models to more accurately predict active TB progression using patients medical data at HIV-1 diagnosis. Training our model involved utilizing clinical data routinely collected at enrollment from the Swiss HIV Cohort Study (SHCS). This dataset encompassed 55 PWH who developed active TB six months post-enrollment and 1432 matched controls enrolled between 2000 and 2024.

Results
Implementing Random Forest modeling and Area under the Curve (AUC) metrics, we predicted active TB with an AUC of 0.78 (CI 0.76 - 0.8) within the SHCS. External validation utilized data from the Austrian HIV Cohort Study (AHIVCOS), comprising 43 incident TB cases and 1005 controls from the same time. Comparable AUC values of 0.71 for Swiss PWH and 0.68 for Austrian PWH were obtained after adjusting demographic parameters to enhance dataset comparability and re-fitting the model with a reduced parameter set. Comparative analysis against the standard of care for identifying patients at the highest risk demonstrated superior performance to current standard of care (Tuberculin skin test (TST) and Interferon gamma release assay (IGRA)) in terms of the Number Needed to Diagnose (NND) (2.3 vs. 4).

Conclusion
Summarized, the AI algorithm introduced in this study has the potential to diagnose PWH at high risk of active TB in low transmission settings, surpassing the current clinical standard. Because the algorithm relies on standard clinical assessment during HIV-1 diagnosis and does not require any additional laboratory tests, it holds promise as a highly effective screening method.

Aim
The optimal duration of postoperative antibiotic treatment in orthopedic bone and implant infections is unknown. We debride and randomize eligible adult patients since October 2022 into a short vs. a long postoperative antibiotic treatment arm. For this 1st. interim analysis, we evaluate the ITT (intention-to-treat)-population with uncensored follow-up times, emphasizing on failure and safety issues.

Methods
A 1:1 randomization allocates eligible episodes into a short or long postoperative antibiotic group. We treat the short group with 3 weeks of postoperative antibiotic therapy for bone infections and during 6 weeks in case of a retained implant. The long arm represents 6 weeks of therapy for implant-free osteomyelitis; and 12 weeks with residual implants. The outcomes are "clinical failure" (defined as revision surgery for wound problems, new infections or mechanical reasons), "microbiological recurrence" (infection recurrence with identical pathogens) and "serious adverse events" (SAE).

Results
As of the start of 2024, we included 170 infection episodes; 42 episodes (short arm; 3 weeks) vs. 48 cases (long arm; 6 weeks) for osteomyelitis; and 55 (short arm; 6 weeks) vs. 25 cases (long arm;12 weeks) for residual implant infections. The four frequent pathogen groups were Staphylococcus aureus (n=47; 28%), coagulase-negative staphylococci (28%), Gram-negative rods (18%), and various streptococci (9%). The median number of surgical debridement was 1 in all arms. For osteomyelitis, 5 (3/42; 7%) episodes yielded a “clinical failure” in the short and 9 (9/48; 19%) in the long arm (Pearson-χ2-test, p=0.32). The corresponding numbers for implant-related infections were 6/55 (11%) vs. 2/25 (8%), p=0.69, respectively. Overall, we detected 4 (4/170; 2%) "microbiological recurrence", with E. faecalis and P. aeruginosa in two long arms each, and with S. epidermidis and S. lugdunensis in two short arms each. Among the 38 SAEs (38/170; 22%), only 5 (3%) were antibiotic-related. The rest was panoply of various postoperative internist, anesthesiologic and uninfected wound problems. Both C. difficile colitis cases (2/170; 1%) occurred in the long treatment arms.

Conclusion
A shorter antibiotic therapy might be non-inferior when compared to the standard long treatment duration. The SALATIO trials continue and are open for multicenter recruitment.

Background
The Swiss Mother and Child HIV Cohort Study (MoCHiV) is an ongoing prospective, multicentric observational study in Switzerland investigating measures to prevent mother-to-child-transmission in pregnant women with HIV (WWH) and assessing health and development of their exposed children as well as of children with HIV (CWH) in general. As part of the Swiss HIV Cohort study (SHCS, www.shcs.ch) its focus is on interdisciplinary clinical and translational research, epidemiological and social science and public health questions.

Methods
Information concerning pregnancy, delivery and the offspring of pregnant WWH is collected. CWH are followed semiannually until 18 years of age while HIV exposed uninfected children (HEU) are followed annually until 5 years of age. The dataset comprises socio-economic data and detailed information on the health status and therapy of pregnant WWH and their children. Information on pregnancy follow-up and delivery is also available. In addition, characteristics of CWH cover information on HIV-associated diseases, treatment and laboratory results. Blood samples from mothers and children are regularly taken and stored in a biobank.

Results
Between January 1986 and December 2022 a total of 1446 children were born from the 1041 WWH. Median age of women at birth of their first child was 30 years (IQR 25-35) and median age at HIV diagnosis was 26 years (IQR 23-31). Overall, 98 children turned out to be diagnosed with HIV resulting in a vertical transmission rate of 0.7% during the past 37 years. Additionally to the 1446 children mentioned above, data of 708 (521 HIV exposed children and 187 CWH) children without detailed information about the mother have been collected. Of the total 285 CWH enrolled, 95 (33.3 %) were lost to follow-up or voluntarily withdrew from the study (e.g. changed to a physician not participating in the SHCS), 61 (21.4 %) died and 16 (5.6%) are currently still being followed. 113 (39.6 %) children have reached adulthood and are now followed within the SHCS protocol.

Conclusions
MoCHiV provides access to a unique longitudinal data-collection on pregnant WWH, their offspring as well as on CWH. With its ability to answer clinical and translational research and public health questions this cohort has contributed to improve prevention of mother-to-child transmission (PMTCT) and secure optimal care of pregnant WWH and their exposed children, as well as of CWH over the last 30 years.

Aims
The duration of viral shedding in patients with SARS-CoV-2-infection may vary based on the type and extent of immunosuppression, with direct implications on infection prevention and control strategies. Consequently, systematic screening of immunocompromised patients was conducted at our institution before discontinuing isolation precautions. The objective was to evaluate the duration of viral shedding in immunocompromised individuals.
Methods
This single-center, retrospective cohort study was performed at the University Hospital Basel, a Swiss, tertiary referral centre. Immunocompromised patients with detection of SARS-CoV-2 by PCR between 03/2020 and 10/2022 were included. Solid organ transplant recipients, patients with haemato- oncological malignancies, or with neurological, rheumatological, dermatological, gastroenterological or renal disease requiring immunosuppressive treatment and patients on dialysis were considered. Patients with unknown infection onset or detection of a low viral load in line with past infection were excluded. Pertinent clinical data was extracted by medical chart review.
Results
Eligibility criteria were met by 163 patients whose duration of shedding could be estimated with follow- up testing. The main underlying conditions were haemato-oncological malignancies and solid-organ transplantation. Median duration of shedding was 17 days, ranging from 5 to 127 days. Viral shedding ≥28 days was observed in 50 patients (30.7%). Of these, 27 (54%) had an oncological malignancy (22.2% with lung-cancer), 15 patients (30%) had haematological malignancies and 10 (20.0%) were solid organ transplant recipients (50% kidney transplants, 40% lung transplants), with more than one immunocompromising condition being present in 16 patients (32%). 10% of patients with prolonged viral shedding ≥28 days were receiving anti-CD20 monoclonal antibodies.
Conclusion
Viral shedding, as detected by PCR, discontinues within four weeks for the majority of immunocompromised patients (69.3%). Prolonged shedding over four weeks was most commonly observed in patients with haemato-oncological malignancies or solid organ transplantation.

Background
β-lactam antibiotic allergies are a major concern in antimicrobial stewardship programmes because most of patients who referred allergy are not truly allergic and this can lead to inappropriate antibiotic prescriptions. An adequate evaluation of allergy labelling is therefore mandatory to optimize antibiotic treatments in hospitalized individuals.

Aims and Methods
Aim of this study was to analyse information about antibiotic allergy labelling in the clinical records of patients hospitalized in all public hospitals in Ticino between July 1st and December 31st 2023 who received at least one antibiotic treatment during hospitalization. Allergy information analysed included the antibiotic to which the patient referred allergy, the severity of allergic reaction and the symptoms reported.

Results
A total of 437 allergies to β-lactam were reported in 398 patients (median age 73, 95% CI: 35-92 years), hospitalized for a median time of 8 days (95% CI: 2-31 days). 354 (81%) of the registered allergies concerned penicillins and derivatives, 71 (16.2%) cephalosporines, 10 (2.3%) carbapenems, and 2 (0.5%) unspecified antibiotics. In 299 cases (68.4%) no information about the reaction was recorded; 91 (20.8%) had a cutaneous reaction (e.g. rash or urticaria); 26 (5.9%) had anaphylactic reaction or DRESS syndrome. Only 8 cases of allergies (1.8%) were anamnestically confirmed by allergologic tests. The remaining reported symptoms (n=13, 3%) were unlikely being real allergic reactions but side effects of the treatments (as renal or hepatic failure, epilepsy). The allergy information was updated only in 154 (38.7%) patients during hospitalization and in 45 (11.3%) after discharge (median time 21 days, 95% CI: 0-125 days). In the others, the update dated a median of 440 days (95% CI: 6-1370 days) before admission.

Conclusion
Our analysis shows that allergy information in the electronic system is rarely updated during hospitalization; the information provided is usually of poor quality and missing data are predominant, leading to a suboptimal treatment of patients and to an increased use of second-line antibiotics. A proper anamnesis is mandatory to discriminate between real allergies or other symptoms unlikely related to antibiotics. In this context, the de-labelling of allergy becomes almost unfeasible. Efforts should be made by clinicians to ensure that allergy labels are promptly updated and pertinent for making safe antibiotic prescriptions.

Swine influenza A viruses (swIAV) are zoonotic pathogens that cause respiratory infections in pigs and can lead to mild or severe respiratory symptoms in humans. Pigs are susceptible to avian and mammalian IAVs, making them key contributors to the evolution of the virus through genetic shift and/or drift. These evolutionary mechanisms can lead to the emergence of novel strains with pandemic potential in humans. Active genomic surveillance of IAV diversity and transmission at the pig-human interface is relevant for efficient pandemic preparedness. Here, we report a suspected case of a zoonotic swIAV spillover at a pig farm in Switzerland.

On 23 November 2023, five pigs with Influenza-like illness (ILI) symptoms along with the pig farmer, who presented with fading ILI symptoms and tested positive for IAV via RT-qPCR. Notably, the farmer's son experienced severe ILI symptoms two weeks prior to the sampling day.

Whole genome sequence analysis identified swIAV subtype H1N1 in the human and pig samples. Pairwise nucleotide sequence analysis of all six samples showed > 99% similarity across all eight gene segments. HA sequences of all six samples formed a single phylogenetic cluster within the Eurasian-avian-like lineage in clade 1C.2.2. These sequences were closely related to previously isolated swIAV from Switzerland and other European countries.

Taken together, these findings suggest a likely scenario of a zoonotic spillover of swIAV at the pig-human interface. This is the first report of detection of swIAV in human and pig samples from the same farm in Switzerland. Early detection and further understanding the risk of zoonotic spillover events is essential for preventing the emergence of novel influenza strains with pandemic potential.

Aim: To analyze epidemiological trends in the incidence and resistance rates of Citrobacter spp. in Switzerland and its 3 main linguistic regions.
Methods: We conducted a retrospective, nationwide surveillance study on Citrobacter spp. clinical isolates reported by 71 hospitals that participated in ANRESIS from 2010 to 2022. Patient-level data (age, sex, type of specimen collected) and institution-level data (linguistic region of Switzerland, type of hospital) were extracted. We calculated incidence of Citrobacter spp. isolates per 100,000 inhabitants, stratified by the 3 linguistic regions. We evaluated the proportion of isolates with resistance to third and fourth generation cephalosporins, fluoroquinolones, and carbapenems.
Results: From 2010 to 2022, there were 60037 Citrobacter spp. isolates in the ANRESIS database. The median patient age was 65 (IQR: 50-80) years; 51% were female and 58% were outpatients. The incidence of Citrobacter spp. increased significantly from 35 to 80 cases per 100,000 inhabitants (p < .001), as well as in each of the three linguistic regions. C.koseri and C.freundii accounted for 57% and 29% of isolates, respectively. The most frequent source was the urinary tract (70%). An increase in C. koseri urinary tract isolates was observed, rising from 34% (908/2648) in 2010 to 47.5% (3425/7202) in 2022 (p < .001). There were 2137 cases of Citrobacter spp. bloodstream infections (3.6%), with a slowly increasing trend at the national level. This trend was more pronounced in the Italian-speaking region (from 3.9 in 2010 to 5.8 cases per 100,000 inhabitants in 2022; p < .001). Among isolates from intensive care units, between 42 to 55% of C.freundii complex isolates had resistance to third generation cephalosporins. C.freundii also demonstrated a higher proportion of resistance to carbapenems (1.5 to 12.5%) and cefepime (0 to 13%) compared to other species. Most of Citrobacter isolates remained susceptible to fluoroquinolones, between 95 to 98%.
Conclusion: Citrobacter spp. is an emerging pathogen of clinical importance in Switzerland. This observed increase emphasizes the value of monitoring trends of all enterobacterales.

The globally endemic low pathogenic human coronavirus (HCoV) 229E has been circulating in the human population for a long time with little sequence alterations. HCoV-229E-like viruses have been found in bat species (BatCoVs) as well as dromedary camels (DcCoVs) exemplary DcCoV-ACN4. For HCoV-229E and 229E-like DcCoVs no recent zoonotic spillovers are documented. Genome analysis propose that HCoV-229E evolved from bats via dromedary camels. This evolutionary scenario shows strong parallels to the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV). MERS-CoV is a highly pathogenic zoonotic virus that sporadically spills over from the dromedary camel reservoir to humans with a 36% fatality rate. Like HCoV-229E, the origins of MERS-CoV have been linked to ancestral BatCoVs. Consequently HCoV-229E and DcCoV-ACN4 can provide important insight into how emerging CoVs like MERS-CoV cross the species barrier and adapt to the human species.
To analyze potential species barriers, we first investigated the spike-receptor interaction of HCoV-229E and DcCoV-ACN4. We used vesicular stomatitis virus (VSV) CoV-S pseudotyped viral particles on HEK cells overexpressing the human or dromedary camel aminopeptidase N; receptor for HCoV-229E. Then we assessed permissiveness by performing replication kinetics on species-specific cell lines. To mimic in vivo conditions, we further performed the replication kinetics on human (h) and camelid (c) primary airway epithelial cell (AEC) cultures. Proceeding Immunofluorescence staining imply adverse cell tropism for HCoV-229E in hAEC, DcCoV-ACN4 in cAEC and MERS-CoV in hAEC and cAEC.
We show an entry-independent species-restricted replication of HCoV-229E and DcCoV-ACN4 in AEC culture that was not observed for MERS-CoV. Our findings indicate that the observed species barriers of HCoV-229E and DcCoV-ACN4 lie beyond the spike-receptor interaction and open the search for the viral and host factors influencing the different host specificities of HCoV-229E, DcCoV-ACN4 and MERS-CoV.

Aims: In early 2024, an increase in vancomycin-resistant Enterococcus faecium (VRE) ST612 was documented in various parts of Switzerland. We aimed at identifying epidemiological links and determining risk factors for acquisition of this emerging strain.
Methods: Laboratories were asked to share their sequence data or send their VRE strains to the National Reference Center for Antimicrobial Resistance. Of all VRE vanA ST612 cases identified since 2018 we contacted concerned hospitals to collect clinical and demographic data of sporadic cases and local clusters along with information on outbreak investigations. Results are descriptively summarized.
Results: Until April 2024, 106 VRE ST612 cases from 23 institutions have been identified, with predominant occurrence (93%) in the German-speaking part of Switzerland. Detailed data were available for 86 (81%) cases, and revealed 38 (44%) sporadic cases, and 7 epidemiological clusters comprising 48 (56%) cases. Most cases were detected by rectal swab (n=61; 71%) or urine cultures (13; 15%). Most sporadic cases were detected in nephrology (6; 16%), gastroenterology (5; 13%), and general surgery (5; 13%), while attribution of clusters was more scattered. Preceding antibiotic exposure was common in both groups (74%). VRE infections were documented in 2 sporadic cases (5%) and 8 (17%) cluster-associated cases. While the most probable source of acquisition remained unknown in sporadic cases (71%) as well as index cases of clusters (71%), many sporadic cases were previously in contact with the Swiss healthcare system (76%). However, a previous hospitalization abroad was more frequent in the index cases of clusters (29% vs. 3%). The definition of contact patients was heterogeneous, leading to limited data on contact patients beyond immediate roommate screening.
Conclusion: The high proportion of sporadic VRE ST612 cases points to wide-spread dissemination of this clone. This could be due to hidden transmission chains within the Swiss healthcare system, suggesting that more effective control measures including intensified screening cultures of transferred patients and patients with frequent health care exposure are urgently required. Inconsistent tracing of contact patients limits the in-depth investigation of epidemiological links. A unified case report form and a centralized database could leverage identification of epidemiolocal links and early detection of interfacility spread.

Background: Contact, droplet and airborne isolation are terms used in German-speaking countries to describe measures to prevent the transmission of multidrug-resistant organisms (MDRO) or communicable diseases. The term “isolation” should no longer be used for the following reasons: The strict differentiation between droplet and airborne transmission overlooks the continuum of respiratory particles. Additionally, “isolation” practices are associated with impaired patient care, depression, anxiety and with adverse outcomes. This project aimed to replace the term “isolation” with an easy-to-understand terminology that builds on the most important measures, the standard precautions, and integrates new insights into infection prevention practices. The ultimate goal should be to mitigate stigma and adverse outcomes for patients.

Methods: A comprehensive approach was chosen to revise the nomenclature and practices surrounding infection prevention measures. This involved the engagement of infection prevention specialists and other healthcare workers to discuss and redefine terms and procedures based on the latest scientific evidence regarding respiratory particles and practical considerations.

Results: The focus moved from terminology based on transmission routes to a more inclusive and descriptive framework. The initiative led to the replacement of the term "isolation" with "Standard Precautions+," where the “+" signifies additional required actions tailored to specific pathogens or clinical contexts. The new implementation categorizes measures into more intuitive categories, such as "Standard Precautions+ Disinfection Single Room" (formerly contact isolation) or "Standard Precautions+ Surgical Mask Single Room (formerly droplet isolation). This shift simplifies understanding required precautions across all professionals in contact with these patients.

Conclusion: Introducing "Standard Precautions+" represents a significant step forward in infection prevention, offering a more nuanced and adaptable framework that reflects the complexity of pathogen transmission. Early feedback suggests high acceptance and appreciation for the more precise, actionable guidance. This initiative underscores the importance of evolving infection prevention practices in line with scientific advancements and operational realities, potentially setting a new standard for hospitals and healthcare settings worldwide. A evaluation of the measures is planned to close possible gaps.

Objectives: Semi-automated surveillance systems are a time-saving alternative to traditional manual surveillance (1, 2). This is especially true for non-ventilator-associated hospital-acquired pneumonia (nvHAP), an infection all non-intubated patients are at risk for (3). In this study, we aimed to evaluate the performance characteristics of single indicators and algorithms that pre-select patients for manual nvHAP chart review.
Methods: Single indicators were identified based on literature, expert opinion and data availability. They were then combined in simple and complex algorithms. All single indicators and algorithms were applied on a patient cohort of 157,902 patients from a 4-year period. This cohort included 947 patients with nvHAP identified by a validated semi-automated nvHAP surveillance system plus the manual surveillance of patients with ICD-10 discharge diagnostic codes (gold standard). The performance characteristics assessed were sensitivity, specificity, workload reduction, overall performance, and number needed to screen.
Results: Compared to the gold standard, single indicators had a sensitivity from 35.1% (worsening oxygenation) to 99.7% (radiologic procedure). The workload reduction varied from 57.3% (length of hospital stay >5d) to 98.4% (ICD-10 discharge diagnostic code). The single indicator radiologic procedure of the chest was highly sensitive (99.7%) and reduced manual review by 82.8%, or by 90.3% when considering the full text of radiologic reports (sensitivity 99.3%). The highest workload reduction was found in complex algorithms, e.g. the combination "radiologic procedure including full text AND temporally related abnormal WBC or fever AND anti-infectives AND CRP AND decreased oxygenation AND stay ≥5 days AND no intubation" had a workload reduction of 96.2% by maintaining a sensitivity of 92%.
Conclusions: We identified several single indicators and algorithms with a high workload reduction and a sensitivity above the PRAISE-network defined sensitivity threshold of 90% (4). Our results could assist hospitals in developing algorithms customized to their specific local conditions, consequently enabling semi-automatic surveillance of nvHAP.

Background: The cost-effectiveness of systematic latent tuberculosis infection (LTBI) screening for healthcare workers (HCWs) in low-incidence Tuberculosis (TB) countries remains unclear. Our study aims to estimate LTBI incidence and management of cases among healthcare employees screened at recruitment in a large Swiss cantonal hospital, as well as lab costs of the screening strategy.

Methods: This retrospective observational study involved all employees in contact with patients newly hired at Valais Hospital from 1 January 2019 to 31 December 2022. LTBI screening was performed using an Interferon Gamma Releasing Assay (IGRA) (QuantiFERON-TB Gold Plus ®). Positive cases were assessed for TB preventive treatment based on specific criteria, including age and additional risk factors, after ruling out TB disease. Data on screening outcomes, treatment acceptance, and associated lab costs were collected and analyzed. LTBI screening strategies in HCWs of several Swiss hospitals through were also collected through a rapid survey among occupational health divisions.

Results: Out of 1 696 IGRA tests performed, 53 (3.1%) returned positive. A third of the positive tests (17/53; 32.0%) were in HCWs that had already been diagnosed with LTBI in the past. These individuals were not offered a TB preventive treatment. A significant proportion of HCWs with positive IGRA (22/53, 41.5%) either did not meet preventive treatment criteria or were lost to follow-up. Only 14/53 (26.4%) individuals were offered a preventive treatment, and only 5 of them (35.7%) started it. One employee who refused the preventive treatment subsequently developed a TB disease. The estimated lab cost of IGRA testing for the 4-year period was CHF 207 929. Five of the seven hospitals surveyed had a LTBI screening policy on recruitment based on the risk of subsequent occupational exposure (employees in contact with patients, laboratory or environment).

Discussion: The low positivity rate of LTBI screening among new employees and the even lower treatment uptake highlight the challenges in managing LTBI in a low incidence setting. Despite rigorous screening policies, ensuring adherence to preventive treatment remains problematic. These findings question the cost-effectiveness and practical value of routine LTBI screening at recruitment in low TB incidence environments, especially considering the strict infection control measures in case of suspected or TB case.

Aim
The perioperative antibiotic prophylaxis with a single-shot of 1st or 2nd-generation cephalosporins is evidence-based in elective orthopedic surgery regarding the prevention of surgical site infections (SSI). There are, however, situations with a high risk of prophylaxis-resistant SSIs. We evaluate the rationale for a broad-spectrum prophylaxis in two specific patient populations with such a high risk: surgery in chronically open wounds and surgery under the influence of concomitant antibiotic therapy.

Methods
Since October 2022, we run a clinical trial randomizing (1:1) eligible adult orthopedic patients into a “standard” (cefuroxime) vs. a broad-spectrum prophylaxis (single-shot of combined vancomycin 1 g & gentamicin 5 mg/kg). In case of concomitant antibiotic therapies, the “standard” prophylaxis either represents cefuroxime or the continuation of the therapeutic agent. We investigate the influence of the prophylactic spectrum on “clinical failures” (defined as surgical revision, persistent or new local problems), secondary SSI with new pathogens, SSI pathogens' coverage by the index prophylaxis, and on the number of Serious Adverse Events (SAE) in each arm.

Results
Overall, 193 episodes received the “standard” prophylaxis and 147 the vancomycin-gentamicin combination. Among infected cases that were iteratively debrided, the proportion of secondary SSIs with new intraoperative pathogens was 17% in the standard vs. 10% in the broad-spectrum arm (Pearson-χ2-test; p=0.03). As a consequence, the clinicians broadened the therapeutic antibiotic regimen in 17% of episodes with prior standard prophylaxis vs. 7% with previously broad prophylaxis (p=0.01). The association with immediate "clinical failures” in the aftermath of surgery was less in the broad-spectrum arm (71 failures / 193 standard prophylaxes vs. 44 failures / 147 broad-spectrum prophylaxes; p=0.18). When considering late failures, the corresponding proportions were 17% and 14%, respectively (p=0.91). The risk for SAEs during and after hospitalization was similar (41 SAEs in the standard vs. 35 SAEs in the broad-spectrum arm; p=0.57).

Conclusion
We saw a tendency to a better general SSI prevention in favor of the broad-spectrum prophylaxis, compared to the standard "protocol"; albeit not significantly. The benefit of the broad-spectrum prophylaxis seems higher for the prevention of future broader-spectrum antibiotic treatments. We continue the BAPTIST trial.

Aims
Current guidelines do not recommend routine surgical antimicrobial prophylaxis (SAP) administration prior to low-risk cholecystectomy (LR-CCE). However, data from large real-life cohorts supporting this recommendation is limited.
Our Aim was to assess whether administration of cephalosporine ± metronidazole SAP versus absence of SAP is associated with a decreased risk of surgical site infections (SSI) in LR-CCE.
Methods
This cohort study included adult patients who underwent LR-CCE, documented by the Swissnoso SSI surveillance system between 1/2009 - 12/2020 at 66 Swiss hospitals, with a completed 30-day follow-up. LR-CCE was defined as elective endoscopic surgery, age < 70, no active cholecystitis, ASA score < 3, operating time < 120 minutes without implantation of foreign material.
Exposure was defined as administration of cefuroxime or cefazoline ± metronidazole within 120 minutes prior incision versus no SAP administration.
Main Outcomes and Measures were the occurrence of SSI until day 30 according to CDC definitions. Logistic regression models were used to adjust for institutional, patient, and perioperative variables.
Results
Of 44 682 surveilled adult cholecystectomy patients, 12 521 (8 726 women [69.7%]; median [IQR] age, 49.0 [38.1 - 58.2] years), fulfilled inclusion criteria. SSI was identified in 143 patients (1.1%): 106 (0.8%) with a superficial incisional, 12 (0.1%) with a deep incisional and 25 (0.2%) with an organ-space SSI. SAP was administered in 9 269 patients (74.0%); mostly Cefuroxime (6 403, 69.1%). Metronidazole was added in 466 patients with SAP (5.0%). SAP was significantly associated with a lower SSI rate (adjusted odds ratio [aOR], 0.49; 95% confidence interval [CI], 0.35 - 0.70; p < .001). Additional analyses showed that SAP administration was associated with a lower superficial (aOR, 0.45; 95% CI, 0.30 - 0.70; p = 0.01) and deep incisional SSI rate (aOR, 0.22; 95% CI, 0.06 - 0.67; p < .001), but not with a lower organ-space SSI rate (aOR, 1.37; 95% CI, 0.54 - 4.18; p = 0.53).
Conclusions and Relevance
Overall LR-CCE SSI rate was low. However, cephalosporine SAP administration was associated with significantly lower risk of LR-CCE SSI, mainly due to lower odds of superficial and deep incisional SSI. Our results suggest that cephalosporine SAP should also be administered in LR-CCE.

Introduction:
Multi-drug resistance (MDR) is a significant public health concern because it complicates the management of infections, leading to higher morbidity, mortality, and healthcare costs.
Inadequate infection control measures or lack of awareness of colonization can lead to exposure with MDR in the inpatient setting. Guidelines do recommend to actively screen these contact-patient to identify possible transmission. We examine transmission rates in our own cohort of contact-patients.

Methods:
This retrospective study was conducted at a medium-sized 400-bed hospital in Switzerland. We maintain a systematic database of all patients colonized with multi-drug resistant (MDR) organisms since January 2022. Patient whose MDR-colonization was initially unknown were identified. Then contact-patients were searched using the electronic-medical record database. The criteria for defining a contact and the subsequent procedures followed are in alignment with national guidelines published in 2021. Statistical analysis was conducted to describe the population of index-patients as well as contacts-patients and possible transmissions.

Results:
We identified 112 index patients, of which 47 were either outpatients or had no contacts. The majority of the index cases were colonized with MRSA (86), followed by CPE (13 cases) and VRE (7 cases). In total, we found 117 contact patients. The mean number of contacts was as follows: CPE: 1.13 contacts, MRSA: 2.15 contacts, and VRE: 1.75 contacts, respectively. CPE had a mean contact time of 3.31 days, MRSA had a mean contact time of 2.27 days, and VRE had a mean contact time of 2.0 days. All contacts of CPE were screened and were negative. Only 27% of MRSA contacts were screened. One MRSA contact was positive, but genotyping did not show a correlation to the index case. None of the VRE contacts were screened.

Conclusions:
In our retrospective analysis, we observe that active follow-up of MDR contacts succeeds in only a limited portion of the population. The reasons for this may be multifaceted. Primarily, many contact patients have already been discharged by the time we became aware of the indication for screening.
Nevertheless, the yield from the contact screenings that were conducted was very low. Given the expenses and costs this incurs, we are questioning the current approach.
In need of further data, we plan to conduct a prospective analysis of contact patients.

Background: Swissnoso emphasizes the critical role of enhanced infection prevention measures, including isolation and tailored assessments by the infection prevention team, for discontinuing isolation in the context of managing carbapenemase-producing Enterobacteriaceae (CPE). This study evaluates the duration until de-isolation in a real-world setting.

Methods: This analysis included inpatients and outpatients at the Cantonal Hospital of St. Gallen with an initial CPE detection between February 2012 and February 2023, who underwent at least one follow-up screening. We examined patient and isolate baseline characteristics, the number of follow-up screenings, and the time from initial detection to de-isolation or the last control screening. The study also evaluated the incidence of screening failures among de-isolated patients.

Results: Among 121 patients diagnosed with CPE, 55 received at least one follow-up screening. Of these 55, 40 were male (73%). The median age at initial detection was 60 years (range: 15-84 years). Acinetobacter spp. (n=21; 38%) and Klebsiella pneumoniae (n=13; 24%) were the predominant pathogens identified. The initial detection was most commonly gastrointestinal (n=28; 51%). Among 40 patients (76%) without de-isolation, median follow-up was 11 months (range: 0-81 months) with a median of 1 screenings (range: 1-13). Among 15 patients (27%) with de-isolation, median follow-up was 22 months (range: 10-85 months) with a median of 3 screenings (range: 1-9). Post-de-isolation screenings in 7 patients (47%) revealed no failures.

Conclusion: The median time to de-isolate CPE carriers in this real-world cohort exceeded two years, highlighting a reluctance to end isolation after initial detection, underscored by an extremely broad range. In this small sample, no re-detection of CPE was observed after de-isolation. Further investigation and systematic follow-up are necessary to assess the safety of reducing isolation duration and to define criteria for discontinuing isolation.

Ziele
Nosokomiale Infektionen stellen im Spitalalltag eine grosse Herausforderung dar. Um die Umsetzung der Hygienevorschriften auf den Abteilungen zu verbessern, arbeitet die Inselgruppe mit hygienebeauftragten Personen (HP). Dies sind Personen die auf Pflegeabteilungen tätig sind aber vertieft in Infektionsprävention geschult wurden. Um diese in ihrer Rolle besser unterstützen zu können, und den Informationsfluss zu verbessern, wurde ein Merkblatt mit den möglichen Aufgaben einer HP sowie ein Newsletter eingeführt. Da dies als sehr positiv rückgemeldet wurde, stellte sich die Frage: Wie kann die Spitalhygiene eine hygienebeauftragte Person befähigen, ihre Rolle im Alltag umzusetzen und welche konkreten Massnahmen zur Unterstützung können dafür geplant und implementiert werden?
Methode
Es wurde eine Literaturrecherche, sowie qualitative Interviews mit sechs hygienebeauftragten Personen durchgeführt. In den Interviews konnten die hygienebeauftragten Personen ihre Wünsche und Bedürfnisse äussern, welche für die Ausübung ihrer Rolle unterstützend wären. Die Interviews erfolgten im Einzelgespräch während maximal 45 Minuten.
Resultate
In den Interviews zeigt sich: Zeit und ein klarer Rahmen sind zentrale Faktoren, damit die HP sich in ihrer Rolle ausleben können. Um ihre Tätigkeit sicher ausüben zu können, benötigen sie das Wissen und die Unterstützung durch die Spitalhygiene. Alle interviewten HP zeigten sich sehr motiviert. Die hohe Arbeitsbelastung aufgrund der Personalmangellage wird als Limitation in der Umsetzung der Funktionserfüllung wahrgenommen ist. Eine stärkere Gewichtung des Themas Infektionsprävention im Alltag wäre ebenfalls unterstützend. HPs wünschen sich mehr Informationen, Materialien, Unterlagen oder Arbeitsinstrumente von der Spitalhygiene, um ihre Aufgaben besser umsetzen zu können.
Schlussfolgerung
Der wiederholt erwähnte Wunsch nach mehr Arbeitsinstrumenten wurde aufgenommen: Es wurde im Hygieneordner ein neuer Bereich (in Form einer Kachel) implementiert, welcher für die hygienebeauftragten Personen gedacht ist. Darin erhalten die HP Informationen zu Schulungs-/Weiterbildungsangeboten, Checklisten um Überprüfungen oder Einführungen strukturiert durchführen zu können, Informationsblätter welche sie zu Schulungen oder für Themenwochen benutzen können und eine Ablage von Newslettern, damit auch neue HP an ältere Informationen kommen. Damit sollen HP Informationen niederschwellig und ohne grossen zeitlichen Aufwand abholen können.

Aims: The number of patients with multidrug-resistant organisms (MDRO) is rising worldwide. Low-prevalence regions attempt to prevent hospital introduction of MDRO by patients repatriated from high-prevalence healthcare settings by screening and isolation. We aimed to quantify the percentage of MDRO carriers among repatriated patients, identify factors associated with MDRO carriage, and evaluate the yield of MDRO detection per screened body site.

Methods: This retrospective cohort study was conducted at a tertiary care center in Switzerland and included adult patients who had spent more than 24 hours in a healthcare institution abroad. These patients underwent screening for MDRO carriage, with samples taken from standard sites such as the nose and throat, groins, and, starting from mid-2018, the rectum. Additionally, samples were collected from risk-based sites including wounds, urine, and tracheal secretions. MDROs were defined as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), extended-spectrum β-lactamase (ESBL)- and carbapenemase- producing Enterobacterales (CPE), multidrug-resistant (MDR) Enterobacterales, and MDR nonfermenting gram-negative rods. Risk factors for MDRO carriage were assessed using multivariate logistic regression.

Results: Between May 2017 and April 2019, 438 patients were screened and 107 (24.4 %) tested positive for an MDRO, primarily for ESBL-producing and MDR Enterobacterales. Risk factors for MDRO colonization were the length of stay in a hospital abroad, region of hospitalization abroad and antibiotic use categorized by the WHO as 'Watch' and 'Reserve'. Rectal swabs had the highest yield for detecting patients with MDR intestinal bacteria, while nose/throat and groins, or wound samples showed higher sensitivity for MRSA or nonfermenting gram-negative organisms, respectively.

Conclusions: We identified risk factors for MDRO carriage and body sites with the highest yield for a specific MDRO, which might help to target screening and isolation and reduce screening costs.

Background and Aim
The national strategy to combat antimicrobial resistance 3 is currently focusing on the implementation of antibiotic stewardship in Swiss Hospitals and is supported by associations of various professional groups (Swissnoso 2023).
The aim of this project was to assess the potential of antibiotic stewardship interventions by clinical pharmacists in geriatric medicine.

Methods
Over a period of three months (01/2024 - 03/2024), each antibiotic prescription was assessed by a clinical pharmacist. Interventions were suggested to the physician and the implementation rate was calculated. Indication and choice of substance were described.

Results
In total, 409 antibiotic prescriptions were assessed. In 21 % of the prescriptions, the clinical pharmacist had suggestions for changes in therapy. For 16 % (66/409) of antibiotic prescriptions, recommendations were communicated. 66 % of the recommendations were implemented or lead to other therapy adjustments.
32 % of antibiotics were prescribed for pneumonia, 27 % for urinary tract infections and 10 % for bacteraemia including (uro)-sepsis. Ceftriaxone was the substance used the most (26 %), followed by amoxcillin/clavulanic acid (24 %) and piperacillin/tazobactam (17 %).

Conclusion
Clinical pharmacist can contribute to optimize antibiotic therapy, especially in wards with mainly uncomplicated infections such as pneumonia and urinary tract infections. The high implementation rate highlights the acceptance of this interprofessional treatment approach. This indicates that existing structures of various professional groups should be expanded for antimicrobial stewardship activities.